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Descriptions

Data from nuclear ribosomal internal transcribed spacer regions (nrITS) and chloroplast DNA
(cpDNA) have failed to resolve phylogenetic relationships in Pinus. To provide greater
interspecific resolution, five low-copy nuclear genes were developed from mapped conifer anchor
loci. Four genes were sequenced from species representing all Pinus subsections. Individual loci
do not uniformly support the nrITS or cpDNA hypotheses. Combined analysis of low-copy
nuclear loci produces a well-supported subsectional topology. The phylogenetic positions of P.
nelsonii and P. krempfii are of systematic interest. Results strongly support P. nelsonii as sister to
sect. Parrya, and suggest a moderately well-supported position of P. krempfii as sister to the
remaining sect. Quinquefoliae. The most informative locus, a Late Embryogenesis Abundant-like
gene, was used to explore phylogenetic relationships among closely related species in subg.
Strobus. Thirty-nine species were sequenced, with two or more alleles representing 33 species.
Nineteen of 33 species exhibited allelic nonmonophyly in the strict consensus tree. Nucleotide
diversity was strongly associated (P<0.0001) with the degree of species monophyly. While
species nonmonophyly complicates phylogenetic interpretations, this locus offers greater
topological support than cpDNA or nrITS. Lacking evidence for hybridization, recombination, or
imperfect taxonomy, incomplete lineage sorting remains the best explanation for trans-species
polymorphisms. The absence of allelic coalescence is a severe constraint in the application of
phylogenetic methods in Pinus, and taxa sharing similar life history traits may show analogous
patterns. While lack of coalescence may limit their utility in traditional phylogenetics, nuclear
genes remain highly informative in describing speciation events. Pinus chiapensis is a threatened
species originally described as a variety of P. strobus. Prior morphological work suggests P.
chiapensis is a distinct species, but that taxonomy is not universally accepted. Multiple accessions
of three probable progenitors were sequenced at three nuclear loci. No interspecific allele sharing
occurs with P. chiapensis, and its alleles are monophyletic at two loci. Results demonstrate that
P. chiapensis is a distinct species. However, determination of the sister species is complicated by
lack of species monophyly and interlocus variability. Pinus ayacahuite is the least likely
progenitor, but the relationship of P. chiapensis to P. monticola or P. strobus is unclear.